Topics — What a work is about. Nucleation holds whatever reading the owner files here, whether or not an Anthology of the SOTA topic could also hold it; instruction for ML practice belongs to the anthology (ADR-048). The words are seeded from the clusters the reading-time triage of 2026-09-25 found, and grow by decision.
Philosophy of biology — what life, organisms and biological functions are — teleology and function, organisation and closure, biological individuality and autonomy, and the demarcation of the living (group: philosophy; ADR-025).
64 of 2004 LIT documents. Back to the full index.
| # | Title | Summary | Status |
|---|---|---|---|
| LIT-005 v3 | Adding causality to the information-theoretic perspective on individuality | Bourrat (2024), DOI-10.1007/s13194-023-00566-1. Of Krakauer et al.’s (2020) three mutual-information “individuality” terms (A* = I(S_{t+1}; S_t), A = I(S_{t+1}; S_t | E_t), nC = I(S_{t+1}; E_t | S_t)), Bourrat argues that nC and A* are not individuality measures. He then proposes the interventional  = I(S_{t+1}; Ŝ_t) (Eq. 6) and two ETI criteria: C1, a normalised Â_{S2}/H(Ŝ2) ≥ Â_{S1}/H(Ŝ1)|θ₀, and C2, low Var(Â_{S2} | Ê2 = ê2k). None of these is computed on any system. The paper’s claim that  ≡ I(S_{t+1}; S_t | E_t) = A in Krakauer’s model is false in general. | Proposed — read in full 2026-09-25 (NOTE-027); a clear conceptual argument that information-theoretic individuality should be interventional. It is unproven as a measure. Three things would settle it: a worked computation of Â, C1 and C2 on an explicit model (for example Black et al.’s ecological-scaffolding model); a corrected account of how  relates to the observational A; and a correct adjustment set for its own Fig. 3 example. |
| LIT-049 v2 | A coarse-graining account of individuality: how the emergence of individuals represents a summary of lower-level evolutionary processes | Bourrat (2023), DOI-10.1007/s10539-023-09917-x. Bourrat proposes that a partition of particles into collectives defines individuals when the “projected” prediction (coarse-grain at t1, then evolve the coarse-grained state) differs from the “truthful” one (evolve at the fine grain, then coarse-grain at t2) by δC = C_T − C_P < θ, across many traits (Eqs. 1–2). He argues that, because measurement and computation are finite, coarse-graining can be the only way to predict at all: in his example, 100 operations predict 10 entities for 10 timesteps or 2 collectives for 50. That indispensability is his whole case for the “quasi-ontological” status of collectives at Godfrey-Smith and Kerr’s fifth stage. Nothing is computed on any model. | Proposed — read in full 2026-09-25 (NOTE-064); a lucid philosophical statement of “individual = a coarse-graining worth its cost”. Its formal criterion is informal and, as written, degenerate: minimal δC picks the finest partition, and the cost term the argument depends on is never put into the criterion. It would be settled by a worked ETI model in which an explicit accuracy–cost objective is computed and picks out the collectives. |
| LIT-110 v3 | Unknotting reciprocal causation between organism and environment | Baedke et al. (2021), DOI-10.1007/s10539-021-09815-0. The paper gives an epistemic, not a metaphysical, tool for organism–environment reciprocal causation. The loop is “unrolled” into two ordered series of states, O_n and E_n, joined by interventionist (Woodward) causal arrows, and an experienced-environment node Ex_n is added as the interface. Its authors argue that this one diagram keeps an epistemically set organism–environment boundary and maps constitutive, mediational, relational, relocational and physical niche construction onto shared causal patterns. They support this with worked cases, including two multi-species ones (bumblebee–eggplant; rumen microbes–ruminant host). | Active — read in full 2026-09-26 (NOTE-111); worth reading as the clearest statement of the “keep the boundary, unroll the loop” position in the niche-construction reciprocity debate, and as the natural counterpart to Hazelwood (LIT-156); its model is illustrative, not formalized or tested, and the formalization it promises is deferred to later work. |
| LIT-127 v2 | Hutchinson’s ecological niche for individuals | Takola & Schielzeth (2022), DOI-10.1007/s10539-022-09849-y. The paper defines the individualized (ecological) niche as the environmental conditions under which a particular individual has an expected lifetime reproductive success of ≥ 1, counting each offspring as 0.5 per parent in outcrossers. The authors split it into five sub-concepts: realized (A), potential (B), time-slice (C), prospective (D) and trajectory-based (E), plus a “fundamental individualized niche” set aside as practically interchangeable with the potential niche. The individual niche has n + s dimensions, adding intraspecific axes such as density and morph frequency. Its boundary is the expected-LRS isocline of 1, which is estimable only by marginalizing fitness functions across individuals. The authors themselves call the concept “mostly of a metaphorical value”. | Active — read in full 2026-09-26 (NOTE-170); worth reading as the clearest structuring of the “individualized niche” vocabulary, and as the individual-level complement to Trappes (LIT-169); it is a behavioural-ecology position essay, and its own admission that the potential niche is unobservable and estimable only from population-level marginalization limits it to a framework rather than a measurement result. |
| LIT-142 v2 | One or two? A Process View of pregnancy | Meincke (2021), DOI-10.1007/s11098-021-01716-y. Meincke argues that substance ontology forces a binary count of individuals. The Containment View fails empirically, following Kingma. Kingma’s Parthood View either loses foster–neonate identity (“Parts-of-Substances”) or cannot count consistently (“Substances-as-Parts”). If organisms are autopoietic processes, a pregnant individual is instead an asymmetrically bifurcating “hypercomplex” process. The foster is “something in between zero and one” and the whole is “something in between one and two”, and the bifurcation runs on past birth through lactation (“postnatal pregnancy”). | Active — read in full 2026-09-26 (NOTE-115); worth reading as the clearest short worked case of process ontology changing a counting and parthood question, and for its sharp internal critique of Kingma’s Parthood View (§3.2). Its positive view is a programmatic sketch, as the paper itself says (fn 52), and it rests on five process-biology premises that are assumed rather than argued here. |
| LIT-156 v4 | An Emerging Dilemma for Reciprocal Causation | Hazelwood (2023), DOI-10.1017/psa.2023.124. Hazelwood defines RC as “the process of natural selection is both a cause and effect of processes such as niche construction” and EC as “natural selection is an emergent causal process”. He argues they are incompatible. Emergence here is Wilson’s synchronic dependence plus autonomy, cashed out as Pence’s composition. If EC holds, niche construction partly composes selection, so the two fail Woodward’s independent-fixability condition and cannot stand in a causal relation. If EC fails, selection is either non-causal (statisticalism) or individual-level, which is incoherent because relative fitness needs a population (Millstein, Sober). EES proponents should drop RC but can keep niche construction as a genuine cause of the evolutionary product. | Active — read in full 2026-09-26 (NOTE-137); worth reading as a tight, well-sourced argument that brings the reciprocal-causation debate into the composition, exclusion and interventionism literature. Its force depends on accepting a process/product split for selection and a compositional reading of realization, both argued briefly and flagged as contestable. |
| LIT-157 v3 | Reproducees, reproducers, and Darwinian individuals | Bourrat (2025), DOI-10.1007/s11229-024-04880-w. Bourrat builds a nested vocabulary. A reproducee is a B that comes after A, is caused by A, and is of A’s relevant class. A reproducer is a reproducee with reproductive autonomy, meaning it can reproduce across a range of backgrounds. A Darwinian individual is a reproducer with high reproductive causal control, meaning heredity survives as the parent’s description is made finer. On that vocabulary, genes of multicellular organisms are, like hearts, mere reproducees, but with high control. Material overlap is necessary for reproducers, which are whole life cycles, and unnecessary for reproducees, so Griesemer and Godfrey-Smith partly talk past each other. Both quantities get an information-theoretic recipe (conditional MI after Bertschinger et al. 2008 for autonomy; interventional MI across grains, Griffiths et al.’s INF, for control), and neither is computed. | Active — read in full 2026-09-26 (NOTE-100); worth reading as the clearest statement of the reproduced/reproducing distinction and a tidy, well-scoped settlement of the material-overlap dispute. Its value is conceptual. Its two measures are recipes that are never computed, and the autonomy recipe does not match its own verbal definition. |
| LIT-160 v2 | Units and Levels of Selection | Lloyd (2005), https://plato.stanford.edu/ENTRIES/selection-units/. Lloyd’s own four-question anatomy of “unit of selection”: interactor, reproducer (formerly replicator), manifestor of adaptation, and beneficiary. She combines it with a split between two multilevel schools, Wrightian “Evolutionary Change” and Fisherian “Adaptationist/KS”. She uses the two to argue for a verdict, not merely to map the debates. The verdict is that most rejections of group, species and holobiont selection come from demanding that an interactor also be a manifestor of engineering adaptation. By her account, genic pluralism, the ETI models and Godfrey-Smith’s Darwinian populations each fuse roles that should be kept apart. The support is argument plus citation of Wade, Goodnight and others. The entry reports no new results of its own. | Active — read in full 2026-09-26 (NOTE-184); worth reading as the authoritative statement of the interactor / reproducer / manifestor / beneficiary distinction and as a dense map of the units-of-selection literature to 2023. It has to be read as one side’s case. It is not a neutral survey: it argues for the Evolutionary Change school, and it criticises by name several authors this record holds or cites. |
| LIT-167 v3 | The Organism | Baedke (2025), DOI-10.1017/9781009495035. Baedke treats “organism” as a nexus concept with an organizational dimension and a relational dimension, joined by the various kinds of biological individuality. He argues that the standard “persister” (self-maintenance, closure) criterion cannot single organisms out, because colonies, holobionts and ecosystems meet it too, and that organisms are also “overcomers”, able to destabilize and reorganize their own closure. Organisms are then individuated relationally by tracing diachronic causal paths in the unrolled O/E model of Baedke et al. 2021 (LIT-110). The overcomer claim rests on three illustrative cases, anglerfish, sea slug and jumping ant, and is asserted, not shown, to hold of organisms only (p. 40). | Active — read in full 2026-09-26 (NOTE-148); worth reading as a compact, open-access and historically well-informed synthesis of the organism/individuality debate, and as the clearest statement of the persister-vs-overcomer distinction. Its positive account is, in the author’s words, drawn “with rough brushstrokes” (p. 51), so cite it for the problem statement and the distinction, not as having settled organism individuation. |
| LIT-168 v3 | Biological Individuals | Wilson & Barker (2007), https://plato.stanford.edu/entries/biology-individual/. A survey that maps biological individuals by crossing two axes: organism / some parts of organisms / some groups of organisms, against living agent (physiological) / Darwinian (evolutionary) individual. The result is nine regions, each given one example (fruit fly, gene, eusocial colony, lysosome, clade, heart, coral reef, virus, squid+Vibrio). “Part” is never defined, and the entry gives no criterion for which parts or groups count: the placements are the authors’ tentative judgements, “moving from less contentious to more contentious examples” (§7). | Active — read in full 2026-09-26 (NOTE-114); worth reading as the standard map of the biological-individuality literature up to 2023 and the hub for this record’s cluster (LIT-049, LIT-157, LIT-188, LIT-142, LIT-210); it is a survey with one tentative framework of its own, not an argument for a thesis, and for parthood it only supplies examples. |
| LIT-169 v2 | Defining the niche for niche construction: evolutionary and ecological niches | Trappes (2021), DOI-10.1007/s10539-021-09805-2. Trappes compares NCT’s evolutionary niche with the ecological niche. The evolutionary niche is the sum of selection pressures on a population (Odling-Smee, Laland & Feldman 2003), read “externally” as the environmental factors that produce fitness differences. The ecological niche is the conditions that permit continued existence; for a population, mean absolute fitness ≥ 1. Even at their closest, against the realized population niche, the two differ in extension. Habitat degradation is in the evolutionary niche but not the ecological one, and commensalism and non-limiting resources are in the ecological niche but not the evolutionary one. So NCT’s niche is not the “simple translation” of Hutchinson’s niche its proponents claim, and the evolutionary significance of niche construction must be shown case by case rather than following from the definition. | Active — read in full 2026-09-26 (NOTE-155); worth reading as a short, clean conceptual analysis that turns “persistence versus fitness differences” into a precise wedge between two fields’ uses of “niche”; its empirical cases are admittedly thin (the CO2 case is offered as “possible”), and it analyses only the 2003 book’s niche concept. |
| LIT-188 v5 | Scaffolding individuality: coordination, cooperation, collaboration and community | Griesemer & Shavit (2023), DOI-10.1098/rstb.2021.0398. The paper sets out an idealized three-stage sequence of interaction types, which it calls a “first and rough sketch” (§1). Stage 1 is coordination in collections (pairwise, “aggregative” interactions of co-located individuals). Stage 2 is cooperation in conexuses (a connected web of binary interactions whose benefits can still be counted per member). Stage 3 is collaboration in communities: heterogeneous multi-way interactions around a shared goal, in which generatively entrenched “core” interactions give organizational closure. Table 1 puts the transition to a new level of individuality between stages 2 and 3 only. The paper asserts, rather than argues, that this describes evolutionary transitions non-circularly and that individuality is a special case of collectivity. Its one argued conclusion is hedged: community-level inheritance “seem[s] likely to evolve in tandem” with community-level individuality (§3). | Proposed — read in full 2026-09-26 (NOTE-173); a short programmatic sketch, and the authors call it one. It is worth knowing as the compact statement of Griesemer’s scaffolding, reproducer and generative-entrenchment view applied to human social transitions. Its headline claims (non-circularity; individuality as a special case of collectivity) appear only in the abstract. Two things would settle it: the model of community “reliability” and endogenization the authors promise in §2 (“We hope to explore such models in future work”), or an application of the 3Cs to a worked case, such as the companion Neolithic paper (LIT-1935, registered unread), that separates collection, conexus and community by measurable criteria. Re-read 2026-11-01 (NOTE-173, version 3). |
| LIT-192 v2 | What’s at stake in the debate over naturalizing teleology? An overlooked metatheoretical debate | Nahas & Sachs (2023), DOI-10.1007/s11229-023-04147-w. The paper argues that “naturalizing teleology” serves at least two relatively autonomous projects with different success criteria. One is scientific: whether an organism-centred account improves biology, which requires operationalisable models that may trade truth for usefulness. The other is philosophical: whether organismal teleology reshapes the liberal-versus-scientific naturalism debate about mind in nature, which requires truth but no operationalisation. It applies the distinction to one recurring dispute, the demarcation of teleological systems from dissipative structures. In the scientific context, models “cannot and need not” demarcate (§4.1: Cusimano & Sterner; McShea & Babcock). In the philosophical context, preferences between accounts turn on unstated commitments (§4.2: García-Valdecasas’s Aristotelian case for Deacon over the Organizational Approach). | Active — read in full 2026-09-26 (NOTE-094); worth reading as a compact map of organism-centred teleology (the Organizational Approach, Deacon, Walsh, McShea) and for one reusable move, asking which problem an account of goal-directedness is meant to solve. Its positive pluralism is only suggested (“tempting to suggest”, §5), and it is shown on a single dispute. |
| LIT-201 v2 | Alternative formulations of multilevel selection | Damuth & Heisler (1988), DOI-10.1007/BF00647962. Multilevel selection comes in two formulations — MLS1, the effects of group membership on individual fitness, and MLS2, groups’ own tendencies to go extinct or found new groups — which answer different questions about one process, and much of the group-selection and species-selection dispute comes from running them together. | Unavailable — seeded from the abstract on 2026-09-26; a close reading was attempted the same day and found the article paywalled at Springer, with no open, repository or author copy. It stays Unavailable until a copy is supplied. |
| LIT-205 v2 | One equation to rule them all: a philosophical analysis of the Price equation | Luque (2016), DOI-10.1007/s10539-016-9538-y. Luque argues that the Price equation, Δz̄ = Cov(w, z) + E(wΔz) (eq. 1, p. 7), is a Kuhnian “generalization-sketch”, like f = ma. It is not a model, has no predictive power on its own, and becomes empirical only when a specific model interprets it. On that reading the critics’ charges (van Veelen 2005; van Veelen et al. 2012; Nowak & Highfield 2011) that it is “a tautology” and “lacks predictive power” are either false or ask too much, and he recommends that evolutionary biologists adopt it as their unifying framework. | Active — read in full 2026-09-26 (NOTE-101); worth reading as a clear statement of the generalization-sketch reading of the Price equation and as a map of its extensions up to 2015 (Tables 2–3). The philosophical argument is thin in places, notably the Gödel-based case that it is “not a tautology”, so it should be read as one side of the dispute and not as a settlement of it. |
| LIT-210 v2 | Philosophy of Microbiology | O’Malley & Parke (2020), https://plato.stanford.edu/entries/microbiology/. O’Malley & Parke argue in four steps that philosophy should attend to microbes. Microbes do most of the planet’s biological work and underlie every major transition. Microbiology founded medicine, molecular biology and genomics. Microbes are unusually good material models, including for phenomena once defined by animals (predation, ageing, kin recognition, cognition). Microbiome research bears on individuality and causation. They are sceptical about the strongest microbiome claims. Whether host and microbiome form one unit of selection is “still disputed”. Claims that microbiomes change the “self” are “usually expressed in very vague language”. The 2026 revision adds that Asgard-archaea phylogenies may make eukaryogenesis “first and foremost a story about diversification within Archaea” rather than a transition in individuality. | Active — read in full 2026-09-26 (NOTE-159); worth reading as a short, current (April 2026) orientation to where microbes change philosophy of biology, with a useful deflationary check on microbiome-and-self claims. It is a survey with no thesis beyond “pay attention to microbes”; for individuality it points onward to the Biological Individuals (LIT-168) and Units and Levels of Selection (LIT-160) entries. |
| LIT-211 v3 | What Lives? A meta-analysis of diverse opinions on the definition of life | Bender et al. (2025), ARXIV-2505.15849. Three LLMs (Claude 3.7 Sonnet, GPT-4o, Llama 3.3 70B), each run 3 times on both orderings of every pair, rated 68 hand-solicited definitions of life on a −1 to 1 “correlation” rubric. The averaged matrix, cut by complete-linkage clustering at an elbow, gives 8 clusters, 45/68 of them (66%) in “Cognitive Autonomy” (n=24) and “Dissipative Self-Organizing Systems” (n=21). The clusters are weak: the repo’s own saved statistics give an overall silhouette of 0.079, and cross-model agreement is an unadjusted Rand index of 71–79% against a chance level of about 62–74%. The headline that life is “a continuous semantic landscape” is not tested against any alternative. | Active — read in full 2026-09-26 (NOTE-109); worth reading as a dataset: 68 signed, three-sentence definitions of life from named researchers, with a manual thematic coding (Table 1). Its computational conclusions are weakly supported and are better read as illustrations than as findings. |
| LIT-439 | The Computational Boundary of a “Self”: Developmental Bioelectricity Drives Multicellularity and Scale-Free Cognition | Levin (2019), Frontiers in Psychology 10:2688. Proposes “Scale-Free Cognition”: an Individual or Self is the set of parts that pursue a goal together, bounded by the farthest events in space and time it can measure and try to change (its “cognitive light cone”). Selves scale up from homeostatic loops through memory and anticipation, and cells merge into larger Selves by sharing bioelectric state through gap junctions; cancer is the boundary shrinking back to one cell. Because every level that pursues its own goal is a Self, most living systems hold many nested, coexisting Selves, “not one, as implied by Integrated Information Theory”. Levin’s “Self” is a goal-pursuing collective, an agent and an individual in this record’s terms; the essay gives no account of a self as subject. A hypothesis essay: no model and no new data. | Active — read in full 2026-10-02 (NOTE-341); worth reading as the composition-side statement that agency is nested by default: a Self is whatever set of parts pursues a goal together, so cells, organs, organisms and swarms are Selves at once, each bounded by its “cognitive light cone”. It is a hypothesis-and-theory essay with no model, no measurement procedure for the light cone and no data of its own. Its one sentence against IIT’s single-Self picture is asserted in a bracket, not argued, and its consciousness claims are confined to a closing speculation. |
| LIT-526 | Life as we know it | Friston (2013), J. R. Soc. Interface 10(86):20130475. Any ergodic random dynamical system whose states split into internal, sensory, active and external sets with a Markov blanket has internal and active states whose flow can be written as a gradient descent on a variational free energy of the blanket and internal states (Lemma 2.1, Eqs. 2.5–2.8). They therefore “appear” to do Bayesian inference about external states and to bound their own entropy. A simulated “primordial soup” of 128 coupled Lorenz subsystems forms a blanket-enclosed cluster whose internal states predict external motion (5 of 82 above a time-reversed null) and which disperses when blanket or internal states are lesioned. The paper says a candle flame cannot have a Markov blanket, and concedes that the universe holds countless blankets, conjecturing that minimum-entropy blankets mark life. | Active — read in full 2026-10-02 (NOTE-421), from the published text (the author’s posted PDF of the journal version and the PMC full text). Worth reading as the founding statement of the Markov-blanket formulation of the free energy principle applied to life, and as the one text in the record that names a candle flame and says it is not lifelike. Read it as a redescription, not a derivation: its “heuristic proof” shows that the flow of an ergodic system with a Markov blanket can be written as a gradient flow on a variational free energy, by choosing the variational density to equal the posterior. The free energy is variational, not thermodynamic; no heat or entropy production is computed. The simulation is one run, analysed with a blanket chosen by spectral clustering. |
| LIT-528 | Energy flow and the organization of life | Morowitz & Smith (2006 working paper; Complexity 2007). Life may be forced into existence by abiotic free-energy sources, as lightning and hurricanes are channels that relieve electric and thermal potentials. Core anabolism, the reductive citric-acid cycle and the cascade built on it, is read as a relaxation channel for geochemical redox and phosphate energy. Jaynes-style entropy maximization with current-dependent entropies (not entropy-production principles) is offered as the framework, and the emergence of life as a “collapse”, a phase transition of a metastable abiotic earth. Selection on metabolism comes before replication. No quantitative model is given; the authors say the claim is undemonstrated. | Active — read in full 2026-10-02 (NOTE-425), from the Santa Fe Institute working paper (2006-08-029, dated 7 August 2006), not the Complexity version of record. Filed in place of Morowitz’s 1968 book Energy Flow in Biology, which could not be read: every Internet Archive scan of it is lending-only. Worth reading as a short statement of the “life was inevitable” view by Morowitz and Smith: core metabolism, the reductive citric-acid cycle, is a channel geochemistry was forced to open to relieve free-energy stresses, as lightning relieves a charge separation. It is an essay. It says itself that the claim “has not been quantitatively demonstrated”, and its evidence is the structure of core metabolism read in that light. It puts life on a continuum with lightning and hurricanes and draws no principled line. |
| LIT-529 v2 | Incomplete Nature: How Mind Emerged from Matter | Deacon (2011), W. W. Norton. An account of how life, mind and purpose (“ententional” phenomena) emerged from physics, built on constraint and absence rather than on added stuff. Its contents run from absence, homunculi and teleonomy through emergence and constraint to a hierarchy of dynamics (homeodynamics, morphodynamics, teleodynamics), a minimal self-producing system (autogenesis), and then work, information, significance, evolution, self, sentience and consciousness. Unread: registered from the publisher’s description and the contents; the text was not reached. | Unavailable — registered 2026-10-02 from the publisher’s description and a library contents note, not read: no lawful full text could be reached. The Internet Archive scan of the Norton printing is lending-only, and no author-posted draft was found. The companion chapter the record already cites, Deacon & Cashman (2013), “Teleology versus mechanism in biology: beyond self-organization”, is identified below but was not reachable either and is not filed. |
| LIT-530 v2 | What Is Life? The Physical Aspect of the Living Cell | Schrödinger (1944), Cambridge University Press. Lectures given at Trinity College Dublin in February 1943, published as a short book for the lay reader. It asks how events inside a living organism can be accounted for by physics and chemistry. It treats the gene as an “aperiodic crystal” carrying a code-script, defended through the Delbrück model, and in chapter 6 says an organism keeps its order by drawing “order from order” and by feeding on negative entropy from its surroundings. Unread: registered from the publisher’s description and contents; the text itself was not reached. | Unavailable — registered 2026-10-02 from the publisher’s description, the Cambridge Core contents and chapter excerpts, and library catalogue records, not read: no lawful full text could be reached. The book is in copyright with Cambridge University Press. Every Internet Archive scan of a Cambridge or Macmillan printing is lending-only, and the freely downloadable PDFs that turn up (course sites, personal uploads, Internet Archive “opensource” uploads) are unauthorized copies of the Canto edition, so I did not open them. Chapter 6, the negative-entropy chapter, is unread beyond the publisher’s one-paragraph excerpt. |
| LIT-533 | Life as a manifestation of the second law of thermodynamics | Schneider & Kay (1994), Math. Comput. Modelling 19(6–8):25–48. A “restated second law”: systems moved from equilibrium “utilize all avenues available to counter the applied gradients”. Bénard convection and a vortex draining a bottle are read as structures that destroy gradients faster. Life is “another means of dissipating the solar induced gradient” (living systems as “sophisticated mini-tornados, with a memory”), and ecosystems develop to degrade more incoming exergy. A stressed marsh shows smaller flows and fewer cycles; airborne thermal scans show mature forests cooler (degrading 90% of net solar radiation against a quarry’s 62%). The second law is “necessary but not sufficient” for life. | Active — read in full 2026-10-02 (NOTE-415), from the authors’ own formatted text (copyright line “James J. Kay and Eric Schneider, 1992”), not the journal’s typeset version. Worth reading as the canonical statement of the “gradient-dissipation” view of life: living systems and ecosystems are dissipative structures that develop so as to degrade the solar gradient more completely, and the second law is “a necessary but not sufficient cause for life”. Read the thermodynamics as a programme, not a derivation. The “restated second law” is offered as a corollary of Kestin’s stability result but not derived from it. The ecological evidence is one stressed-versus-control marsh pair and a few thermal-scanner and satellite comparisons, all correlational. It draws no line between living and non-living dissipative structures beyond “memory” (DNA). |
| LIT-536 v4 | Biological Autonomy: A Philosophical and Theoretical Enquiry | Moreno & Mossio (2015), Springer, History, Philosophy and Theory of the Life Sciences 12. The book argues that biology should revolve around autonomy, not only natural selection: organisms are organized systems that self-produce and self-maintain as integrated wholes, set their own goals and norms, and promote the conditions of their existence through interaction with their environment. Chapters treat constraints and organisational closure, emergence and inter-level causation, teleology and function, agency, evolution, organisms and levels of autonomy, and cognition. Only the Introduction is read (NOTE-1437): there the authors make closure of constraints the core of biological organisation, say it differs fundamentally from the self-organisation of dissipative structures, and announce that it grounds teleology, normativity and function; the chapters that argue this are unread. | Unfetched — registered 2026-10-02 from the publisher’s description and the chapter list. The book is not open access at Springer. Its only free copy, the authors’ HAL deposit (hal-01151449, hal.science/hal-01151449/document, CC BY-NC 4.0, deposited 13 May 2015), is not the whole book, as this note earlier said: it holds the front matter (Hooker’s Foreword and the contents), the Introduction (pp. xix–xxxiv), the references and the index, and no chapter. The Introduction was read in full on 2026-10-30 (NOTE-1437, Skimmed, because only the Introduction was read). For chapters 1–8 no fuller lawful copy was found: on 2026-10-30 OpenAlex listed the HAL deposit as the book’s only open copy, and the publisher’s chapters are paywalled. HAL also served its anti-bot page to a direct fetch on 2026-10-02 and again on 2026-10-30; the deposit was read from a copy retrieved earlier the same day. It stays Unfetched for the chapters. |
| LIT-566 | Defining Agency: Individuality, Normativity, Asymmetry, and Spatio-temporality in Action | Barandiaran, Di Paolo & Rohde (2009), Adaptive Behavior 17(5):367–386. Three conditions are jointly necessary and sufficient for minimal agency: the system defines its own individuality, it is the active source of modulations of its coupling with the environment (interactional asymmetry), and it regulates that coupling by norms it generates (normativity). Generatively, an agent is an open autonomous system (a precarious network of mutually enabling processes) that adaptively modulates its coupling so as to maintain some of its constituent processes. Minimal life satisfies this; life is sufficient for agency but not necessary. | Active — read in full 2026-10-03 (NOTE-458), from the authors’ own deposit of the accepted text. Worth reading as the standard organizational definition of minimal agency, and as the clearest statement that an agent is not the same thing as an individual. Individuality is one of three conditions, with interactional asymmetry and normativity; it is a precondition for the other two and is not sufficient for agency. The generative definition: an agent is an autonomous organization that adaptively regulates its coupling with its environment and contributes to sustaining itself as a consequence. The paper rejects statistical and energetic measures of asymmetry as sufficient, and says systems optimising an externally fixed function should not be treated as models of agency. |
| LIT-570 | An Organizational Account of Biological Functions | Mossio, Saborido & Moreno (2009), BJPS 60(4):813–841. A trait has a function iff it contributes to the maintenance of a self-maintaining organization, is produced and maintained under that organization’s constraints, and the organization is differentiated. Closure grounds teleology and normativity in the current system, unifying etiological and dispositional accounts. Flames, Bénard cells and hurricanes have closure but no functions, because each makes a single undifferentiated contribution to its own maintenance. | Active — read in full 2026-10-03 (NOTE-444), from the HAL deposit of the submitted version. Worth reading as the organizational account of function and as the place where the organizational school says plainly that a candle flame has closure. Functions are contributions to a differentiated self-maintaining organization by traits that organization produces and maintains. Closure alone grounds teleology and norms but is shared by flames, Bénard cells and hurricanes; organizational differentiation is what functions need. Reproduction is admitted to be a problem and left to a sketch. |
| LIT-582 | Biological organisation as closure of constraints | Montévil & Mossio (2015), J. Theor. Biol. 372:179–191. Two causal regimes act in organisms: processes (thermodynamic changes) and constraints, which act on processes while being conserved at the relevant time scale. Closure is mutual dependence among constraints: each is produced by a process another constraint constrains, and each helps produce another. Closure mixes slow and fast dependence, grounds functions, and is proposed as a boundary criterion. A volume-sweeping count of dependencies, the tendency to closure, separates symbionts that share an encompassing closure, and separated nested closures mark levels of organisation. | Active — read in full 2026-10-03 (NOTE-468), from the authors’ HAL deposit of the accepted text. Worth reading as the paper statement of the central claim of Biological Autonomy (LIT-536): biological organisation is closure of constraints. A constraint is defined by a symmetry: it acts on a process at a time scale at which it is itself conserved. Closure is a set of constraints each of which depends directly on another in the set and generates another, and cannot be split into two closed sets. The paper offers closure as a boundary criterion and gives a preliminary measure, the tendency to closure, for drawing boundaries between interacting organisms. It does not claim closure defines an organism. |
| LIT-709 | Conceptualization of the Holobiont Paradigm as It Pertains to Corals | Goulet, Erill, Ascunce, Finley & Javan (2020), Frontiers in Physiology 11:566968, a review. A coral is a consortium: the animal plus the Symbiodiniaceae, bacteria, archaea, fungi and viruses in its body, mucus and skeleton, and neighbours are excluded by definition. Membership can change, so one colony may be a different holobiont at different times. Traits such as thermal tolerance belong to the host–symbiont combination: not every Durusdinium is heat tolerant, and a novel anemone–alga pairing gave higher oxygen flux under heat than both natural ones. Measuring both partners shows different routes to the same bleaching outcome. Whether the holobiont is the unit of selection is asked, not answered. | Active — read in full 2026-10-04 (NOTE-555); worth reading as a short, explicit statement of why a coral should be studied as a composite of host and microbes rather than as an animal with passengers. It is a mini-review with no data of its own (about 3,700 words), and its strongest point is conceptual: traits such as thermal tolerance belong to host–symbiont combinations, not to either partner. The physiological evidence it cites is thin and partly not from corals: its one demonstration that a combination is “not necessarily the sum of its parts” is an oxygen-flux experiment in the sea anemone Exaiptasia. It poses, and does not answer, whether the coral holobiont is a unit of selection. |
| LIT-721 v2 | Multilevel Selection and the Major Transitions in Evolution | Okasha (2005), Philosophy of Science 72:1013–1025. On how multilevel selection bears on the major transitions in evolution. Unread: the 2022 overview LIT-749 cites it for the two levels at which selection can act during a transition and for the point that the traditional debate set aside the origin of the biological hierarchy. | Unavailable — registered 2026-10-05 from Crossref, not read: no lawful full text could be reached. PhilSci-Archive, which holds the author’s preprint, refused every request and was not bypassed; the journal copy is paywalled; a course copy on an instructor’s personal domain was found and not used. Okasha’s 2022 overview “The Major Transitions in Evolution—A Philosophy-of-Science Perspective” (LIT-749), read in full, cites it for the two-level view of transitions and restates its point that the traditional levels-of-selection debate set aside the origin of the hierarchy. Filed because it is the paper usually cited for multilevel selection in the major transitions. It stays Unavailable until a copy is supplied, not on merit. |
| LIT-740 | Cancer across the tree of life: cooperation and cheating in multicellularity | Aktipis et al. (2015), Phil. Trans. R. Soc. B 370:20140219. Multicellularity rests on five kinds of cellular cooperation, and cancer is cheating on them. Surveying cancer-like growth across the independent origins of complex multicellularity, the authors find division-of-labour cheating in every form, and resource and environment cheating so far only in animals and plants. Complex multicellularity is a cheater detection and suppression system. | Active — read 2026-10-05 (NOTE-562): in full, from the open-access deposit in PubMed Central (CC BY 4.0). Worth reading as a survey of cancer-like growth across the independent origins of multicellularity, read as cheating on five foundations of cooperation: proliferation inhibition, controlled cell death, division of labour, resource allocation and maintenance of the extracellular environment. Cheating on division of labour is reported in every form of multicellularity, and complex multicellularity is described as a cheater detection and suppression system. Limits: a literature review with no model or new data; absences may reflect lack of study, and animals’ apparent susceptibility may reflect sampling. |
| LIT-749 | The Major Transitions in Evolution—A Philosophy-of-Science Perspective | Okasha (2022), Frontiers in Ecology and Evolution 10:793824. A major transition is the evolution of a higher-level unit from formerly free-living units. For one to succeed, higher-level selection must trump selection within the collective, typically through policing or aligned interests. The transitions turn the biological hierarchy from explanans into explanandum, vindicate multi-level selection, and leave the highest occupied level privileged as that of organisms. | Active — read 2026-10-05 (NOTE-586): in full, from the publisher’s open-access PDF (CC BY). Worth reading as a philosopher’s map of the major evolutionary transitions. A transition is the evolution of a higher-level unit from formerly free-living ones; for it to succeed, selection between collectives must come to trump selection within them, typically through policing, kinship or division of labour. The transitions make the biological hierarchy something to be explained rather than assumed, and leave the highest occupied level privileged as the level of organisms. Limits: a review with no model or data, provisional by its own account; it cautions that general principles may explain each transition only coarsely. It stands in for the unread 2005 paper LIT-721. |
| LIT-817 v3 | On the Normal and the Pathological | Canguilhem (1943; expanded 1966; English 1978, reissued 1989), DOI-10.1007/978-94-009-9853-7. Against the nineteenth-century view that disease is a quantitative deviation from a normal state, it argues that the normal is normative: health is an organism’s capacity to institute new norms in a changed environment, and disease a narrowed capacity to do so. Unread: registered from metadata and secondary accounts. | Unavailable — registered 2026-10-07 from metadata and secondary accounts, not read. A lawful full text was sought on 2026-10-14 and not reached. OpenAlex and Unpaywall report the English edition closed. SpringerLink (link.springer.com/book/10.1007/978-94-009-9853-7) serves the front matter and the two section title pages free; the seventeen chapters are subscription content. The front matter was read: the table of contents (which confirms the chapter list in the body), the translators’ note (the translation follows the 1972 PUF edition) and Michel Foucault’s introduction (pp. ix–xx). Foucault’s introduction is an essay on Canguilhem as a philosopher of error and concept, not a summary of the book’s argument, so no NOTE is filed from it. It does not state what CLAIM-018 cites it for, health as a capacity to institute new norms. The French editions are in copyright, and no author-sanctioned copy was found. It stays Unavailable until a copy is supplied. |
| LIT-990 v3 | Agency, Goal-Directed Behavior, and Part-Whole Relationships in Biological Systems | Watson (2023). A perspective essay offering a scale-relative, comparative notion of agency. Relative to a chosen decomposition into parts with goals, a whole is agential with respect to its parts when its organization makes them better at resolving their mutual constraints than they would be at the equilibrium of the old organization. This shows as delayed gratification. Citing earlier models, it argues that unsupervised, bottom-up learning among self-interested parts can produce such organization, so that “the agent creates itself”. It sets no absolute threshold. | Active — read 2026-10-14 (NOTE-747) in full; worth reading as a comparative, scale-relative notion of agency. Given a decomposition into parts with goals of their own, a whole is more agential than its parts when its organization lets them resolve more of their mutual constraints than the old organization did, shown as delayed gratification (going uphill in a specific direction to reach lower minima). Read it knowing that it is a perspective essay. Its model results (Hebbian self-modelling networks, social and ecological networks) are reported from earlier papers. It sets no threshold for an additional agent, and its measure depends on a stipulated choice of parts and of their goals. Learned origin of the organization is offered as an optional restriction, not a requirement. |
| LIT-1017 | Autopoiesis, Adaptivity, Teleology, Agency | Di Paolo (2005), Phenomenol. Cogn. Sci. 4(4): 429–452. Autopoiesis read as conservation gives only an all-or-nothing norm that an observer can see and the system cannot use. Adaptivity, a graded capacity to detect and reverse tendencies toward the boundary of viability, gives good, neutral and bad ways of staying alive, for the system. Behaviour is the regulation of coupling, and agency is behaviour serving viability. | Active — read in full 2026-10-13 (NOTE-719) from the publisher’s typeset PDF that the author posts on his own site (ezequieldipaolo.net/wp-content/uploads/2011/10/autopoiesis_teleology_2005.pdf); the Sussex figshare record that OpenAlex and Semantic Scholar point to holds no file. Registered at the owner’s request from the survey of the Mathematics of Meaning corpus, for CLAIM-079, CLAIM-099 and CLAIM-075. Worth reading as the source of the robustness/adaptivity distinction and of the enactive definition of agency as regulation of coupling. Its norms are norms for the system, and it agrees with CLAIM-075 that viability alone yields none the system can use; it does not separate adaptivity from the capacity to transform it, so it is not evidence for CLAIM-025. |
| LIT-1018 | Life after Kant: Natural purposes and the autopoietic foundations of biological individuality | Weber & Varela (2002), Phenomenol. Cogn. Sci. 1(2): 97–125. An essay arguing that Kant’s natural purposes, Jonas’s metabolism and autopoiesis converge on an intrinsic teleology: a self-producing system’s maintenance of its identity is its purpose, and gives it a point of view and a world of value for it. Autopoiesis is defined for the cell, whose components “constitute the system as a distinguishable unity”; a multicellular organism is said not to be autopoietic itself. No test tells a produced boundary from an imposed one. | Active — read in full 2026-10-13 (NOTE-720) from the publisher’s PDF posted on the site of the IAS-Research Centre for Life, Mind and Society (ias-research.net/wp-content/uploads/2018/02/Weber_Varela_Life_after_Kant_2002.pdf), a research group’s page at the UPV/EHU; OpenAlex and Semantic Scholar report no open-access copy. Registered at the owner’s request from the survey of the Mathematics of Meaning corpus, for CLAIM-194 and CLAIM-075. Worth citing for the autopoiesis definition, whose second clause has the components constitute the system as a distinguishable unity, and for the cell making its membrane. It gives no test that tells a produced boundary from an imposed one, and it says a multicellular organism is not itself autopoietic. Its intrinsic teleology is value for the organism, though one paragraph runs on to a right to life. |
| LIT-1026 | Organizational Accounts of Malfunction: The Dual-Order Approach and the Normative Field Alternative | Barandiaran (2025), Biological Theory 21(1). Argues the dual-order account of malfunction (Saborido, Moreno and Mossio, as stated in Moreno and Mossio 2015) is unnecessarily complicated and too narrow, and offers a ‘normative field’ over the viability space, after Ashby, as the alternative: a trait functions when it correlates positively with the minimum change viability requires, and subfunctional, malfunctional and nonfunctional are three ways to fail. Regulatory traits can malfunction by the same standard. | Active — read in full 2026-10-13 (NOTE-730) from the author’s accepted manuscript on PhilSci-Archive, released under GFDL and CC BY-SA (philsci-archive.pitt.edu/24977/); the Springer typeset version was not seen. Registered from the 2026-10-13 exchange on meaning operators and selfhood (the workbench entry of 2026-10-13, 21:29). Worth reading as the organizational account of malfunction that needs no second order of norms: a graded normative field over the viability space, against which regulatory traits can fail too. It gives QUESTION-087 a standard the organization itself supplies, the whole’s viability, and so cannot tell merited trust from entrenched authority where both keep the organization equally viable. Its norms are for the organism, in agreement with CLAIM-075. |
| LIT-1027 | Genealogies of organizational closure: from logical paradox to mind in life | Rubin, Roli, Stano and Damiano (2026), Frontiers in Artificial Intelligence 9. A genealogy of the notions of closure from mathematical logic, cybernetics, systems theory, thermodynamics, relational biology and the biology of cognition, showing that each closes a different thing. It then argues that closure is a circular organization of efficient causes, distinct from feedback, self-organization and catalytic cycles and not exhaustively describable as a state-determined syntactic procedure, and that current AI approximates closure without instantiating it. | Active — read in full 2026-10-13 (NOTE-727) from the publisher’s open-access PDF under CC BY (frontiersin.org/journals/artificial-intelligence/articles/10.3389/frai.2026.1806435/pdf). Registered from the 2026-10-13 exchange on meaning operators and selfhood (the workbench entry of 2026-10-13, 21:29). Worth reading as a map of what each notion of closure closes (information, operations, efficient causes, constraints, catalysts) and where each came from. Its thesis, closure as circular production of efficient causes that no state-determined syntactic description captures, supports CLAIM-288 and goes beyond it: a system whose objectives its own processes revise is still, on this account, not closed. It gives no test for QUESTION-086, and its non-computability claim rests on Rosen, unassessed. |
| LIT-1029 | Autonomy, Function, and Representation | Bickhard (2000), Communication and Cognition – Artificial Intelligence 17(3–4). A far-from-equilibrium system’s contributions to its own maintenance are functions for it, with function and dysfunction fixed by the asymmetry between persisting and decaying; a candle flame qualifies. A recursively self-maintenant system, one that switches among self-maintaining processes as its environment changes, has representation: indications that an interaction will succeed, which can be false by the system’s own lights. Etiological, informational and Dretskean accounts are rejected as epiphenomenal or observer-dependent. | Active — read in full 2026-10-13 (NOTE-729) from the author’s manuscript text on his Lehigh site (https://www.lehigh.edu/~mhb0/autfuncrep.html); the printed issue was not compared. Worth reading as a compact statement of the organizational account of function before Mossio et al., and of interactivism: function is contribution to a far-from-equilibrium system’s own persistence, relative to that system, and representation is an indication of interaction success that the system can find false. It supports the premise of CLAIM-288 by a second route, gives QUESTION-087 an intrinsic standard bounded by persistence (so it agrees with CLAIM-075), and is vocabulary, not evidence, for CLAIM-284. |
| LIT-1030 v2 | Experimental probes of autopoietic self-maintenance | Segura (2026), BioSystems 268. Unread. The SSRN abstract recorded in Crossref describes a topos-theoretic formalization of probing an autopoietic system (Yoneda lemma, probe profiles, sheaf cohomology) that separates the system’s organization from models of it and from the responses experiments elicit. An earlier description, that assay agreement fixes organization only for assay sets conservative for a class of models, and the exchange’s gloss, that resilience does not show closure, are not in that abstract and are unconfirmed. | Unfetched — filed 2026-10-13, not read. Registered from the 2026-10-13 exchange on meaning operators and selfhood (the workbench entry of 2026-10-13, 21:29), for QUESTION-086. No NOTE is filed, and it stays Unfetched until it is read, not on merit. Looked for a lawful full text on 2026-10-13 and found none that could be fetched: the Elsevier version of record is paywalled; OpenAlex, Semantic Scholar and Unpaywall give one open copy, the SSRN preprint (doi:10.2139/ssrn.6864481, ssrn.com/abstract=6864481), but SSRN answered every request, the abstract page and the delivery links, with a Cloudflare challenge (HTTP 403, cf-mitigated: challenge) that needs a browser running JavaScript, so it was not tried further; Europe PMC (PMID 42637075) has no full text; arXiv, Zenodo and a web search for the title found no other copy; the author’s ORCID record lists the work by its two DOIs and links no other copy. A human reader can likely open the SSRN copy. The SSRN abstract, in its Crossref record, describes a Yoneda-lemma formalization in a topos: an organization is identified by its profile of admissible experimental probes, self-maintenance is invariance of that profile under a production functor, viability is an internal modality, and sheaf cohomology diagnoses whether local responses glue into a whole. The filing’s summary (model-relative assay sets, and the warning that resilience does not show closure) is not in that abstract and is unchecked. |
| LIT-1031 v2 | An Enactive Approach to Artificial Intelligence and Legal Responsibility | Benthall and Salge (2026), SSRN working paper. Going by the authors’ blog post only: on an enactive account mind is tied to self-producing, precarious viability, on which current AI systems are not living systems, and attributing sentience or duties to them could shield their makers from liability. | Unfetched — filed 2026-10-13, not read. Registered from the 2026-10-13 exchange on meaning operators and selfhood (the workbench entry of 2026-10-13, 21:29), for CLAIM-284. No NOTE is filed, and it stays Unfetched until it is read, not on merit. Looked for a lawful full text on 2026-10-13 and found none reachable: the SSRN abstract page and both SSRN delivery URLs (Delivery.cfm?abstractid=7571720, with and without a mirror id) returned 403 “Content Blocked” to curl and to a web fetch; OpenAlex (W7221007972, doi:10.2139/ssrn.7571720) lists the SSRN posting as green open access under CC BY but gives no PDF URL and no other location; Semantic Scholar does not hold it; an arXiv author query for Benthall and Salge found nothing; PhilArchive and CORE returned bot challenges; Benthall’s blog post of 2026-10-09 links only to SSRN, and his site sbenthall.net does not list it; Salge’s site christophsalge.org did not connect (proxy 502) and the Hertfordshire research portal returned 403; web searches found no other copy. A lawful copy exists (SSRN, CC BY) that this client could not fetch. The Crossref record (doi:10.2139/ssrn.7571720, posted 2026) carries the abstract, which confirms the four tests the filing could not: self-production, organizational closure, precariousness and boundary formation, as tests for constitutive autonomy, taken as the physical property that coincides with intrinsic motivation, which the authors make a condition of legal responsibility; the tests are applied to children, corporations, autonomous vehicles, agents built on large language models and prospective autonomous AI systems. |
| LIT-1190 v2 | The physics of symbols: bridging the epistemic cut | Pattee (2001). Evolution requires an epistemic cut between energy-degenerate, rate-independent genetic symbols and the rate-dependent dynamics of construction they control; the same subject–object cut recurs wherever symbols stand for referents, and physics meets it as measurement. Measurement codes a dynamical state into quiescent symbols and control is its converse; both are executed by non-integrable constraints, whose function is lost if they are described by the laws alone (von Neumann’s regress). The cut is epistemic, not ontological, and arises first at the genotype–phenotype control interface. | Active — read 2026-10-16 in full (NOTE-952), from the author-posted text on the Binghamton CASCI site. Worth reading as Pattee’s own retrospective statement of the epistemic cut: measurement codes a dynamical state into quiescent symbols, control is its converse, both are executed by non-integrable constraints, and no dynamical description of those constraints keeps their function. Read it knowing that it is not measurement-first: the primeval cut is at the genotype–phenotype control interface and “control of construction came first”, and measurement presupposes control of the measuring device. The argument rests on von Neumann’s regress and Pattee’s earlier papers; nothing is derived here. |
| LIT-1225 v2 | Division of labour and the evolution of extreme specialization | Cooper & West (2018). A kin-selection model of division of labour over one cooperative trait: it needs accelerating returns to helping but is not guaranteed by them, and when it evolves one phenotype is always a pure reproductive, with a feedback driving helper and reproductive to the extremes. Relatedness does not affect whether it evolves for an essential trait and favours sterile helpers. The authors infer that it drives major transitions. | Active — read 2026-10-29 (NOTE-1369) in full, from the authors’ accepted manuscript in the Oxford University Research Archive; worth reading as the model in which division of labour, once favoured, always yields a pure reproductive and often a sterile helper, with relatedness irrelevant to whether it evolves for an essential trait. Read it knowing that the proofs and simulations are in a supplement not read, that its Table 1 and Figure 5 disagree on how efficiency affects the proportion of helpers, and that it shows dependence, not the vulnerability to losing a specialist that A46 attributed to it. |
| LIT-1227 v2 | The Limits of the Self: Immunology and Biological Identity | Pradeu (2012). The immunological theory that an individual is defined by self and nonself fails, since immune responses to self and tolerance of foreign entities are the rule; Pradeu proposes a criterion of immunogenicity by discontinuity, and from it an immunological account of biological individuality. | Unavailable — filed 2026-10-18, not read. A lawful full text was sought on 2026-10-29 and not reached. OpenAlex reports the book closed. The HAL record it lists, hal-01343696, is a notice with no file deposited (HAL API, 2026-10-29); its other location is an institutional e-book handle that needs a licence. Oxford Academic offers it only to subscribers, and web searches found reviews, paid e-books and Pradeu’s earlier papers, not the book. It stays Unavailable until a copy is supplied. |
| LIT-1241 v2 | Simon-Ando Decomposability and Fitness Landscapes | Shpak, Stadler, Wagner & Altenberg (2004). States Simon and Ando’s theorem on nearly decomposable linear systems, without proof and without rates, as four time windows separating within-block relaxation, block quasi-equilibrium, aggregate cross-block dynamics and global equilibrium. It applies an entrywise version of the condition to mutation–selection and recombination on fitness landscapes. Point mutation meets it at low mutation rates, trivially, and recombination rarely does. It concludes that Simon–Ando aggregation is one route to a dynamically sufficient aggregate, independent of exact aggregation by symmetry and of character aggregation under linkage equilibrium. | Active — read 2026-10-20 (NOTE-977) in full, from arXiv:q-bio/0403030v1; worth reading for the record’s only open statement of Simon and Ando’s (1961) theorem (Theorems 2.1, 2.2a and 2.2b: block-diagonal A* plus εC, the four time windows T0 < T1 < T2 < T3, and the aggregate Â_IJ = Σ_{i∈I}Σ_{j∈J} A_ij ν*_jJ), for its four-stage account of when a nearly decomposable system is decomposable, aggregable or both, and for its conclusion that quasi-equilibrium, symmetry (equitable partitions) and linkage equilibrium are independent routes to a dynamically sufficient aggregate. Read it knowing that the theorem is quoted without proof and states no rate in ε and no bound on aggregation error; that the landscape “Simon–Ando condition” is an entrywise proxy, met trivially at low mutation rate even on a flat landscape where there is no time-scale separation; that its leading-eigenvector statement fails when block leading eigenvalues coincide, the stochastic case it invokes; and that (6.2b) is wrong for radius κ ≥ 2. Published as Theory in Biosciences 123(2):139–180 (2004), doi:10.1016/j.thbio.2004.04.001. |
| LIT-1242 v2 | Aggregation of Variables and System Decomposition: Applications to Fitness Landscape Analysis | Shpak, Stadler, Wagner & Hermisson (2004). Separates aggregation of variables, a lower-dimensional map whose dynamics close and which may depend on every microvariable, from decomposition of a system into subsets of variables, and treats systems that are both as a special case, with applications to fitness landscapes. | Active — read 2026-10-20 (NOTE-979) in full, from the authors’ manuscript in Leipzig University’s repository; worth reading for the distinction between aggregation (a closed lower-dimensional description) and decomposition (non-interacting subsets), for the exact condition under which a partition’s block sums close in a linear system (column-equitability, THEORY-755), and for its application to fitness landscapes, exact for one or two peaks and not for three. Read it knowing that it treats exact aggregation only, paraphrases Simon–Ando without an error bound, states Result 1.1 in a form that fails for some real 2×2 matrices, and overstates in its discussion that every linear aggregation is an equitable partition. |
| LIT-1356 v2 | What Is Enactivism? | Ward (2026). Treating “enactivism” as an umbrella for any view that stresses sensorimotor loops ignores what sets apart the enactive approach of Varela, Thompson and Rosch: life–mind continuity, the primacy of lived experience, and reciprocity between science and self-understanding. A second axis, organicist against informationalist, runs across the cognitivist–embodied one. Embodied predictive processing, extended functionalism and cybernetics are embodied and informationalist; the enactive approach is organicist. A taxonomy, not an argument that organicism is true. | Active — read in full 2026-10-22 (NOTE-1065) from the author’s accepted manuscript in the University of Edinburgh repository; worth reading as a short, clear map that separates where a view puts cognition’s processes (skull, or brain–body–world) from what it says meaning depends on (information, or organization distinctive of living things). On that map embodied predictive processing, extended functionalism and cybernetics are embodied but informationalist, and the enactive approach of The Embodied Mind is organicist, further marked by the primacy of lived experience and by reciprocity, in which the vocabularies we understand ourselves with reshape the experience they describe. Its main limit is that it argues for a taxonomy, not for organicism, and gives no criterion for which properties are distinctive of life. It does not discuss brains in vats, development or grounding. |
| LIT-1656 v2 | Autopoiesis and Cognition: The Realization of the Living | Maturana & Varela (1980). A living system is an autopoietic machine: a network of processes producing the components that, through their interactions, regenerate the network and constitute it as a unity in space. Organization (the relations that define the unity) is distinguished from structure (the components realizing it), and cognition is identified with the process of living. | Unavailable — filed 2026-10-27, not read. A close reading was attempted on 2026-10-27 and no lawful full text was reached: the book is closed on Unpaywall (Springer), with no open copy listed. It stays Unavailable until a copy is supplied. |
| LIT-1669 v2 | Life Itself: A Comprehensive Inquiry Into the Nature, Origin, and Fabrication of Life | Rosen (1991). Organisms are relational systems; in the metabolism–repair ((M,R)) model an organism is closed to efficient causation, every efficient cause of its constitutive processes being produced within it, which Rosen argues no mechanism (a system with a computable model) can be. | Unavailable — filed 2026-10-27, not read. A close reading was attempted on 2026-10-27 and no lawful full text was reached: the book has no DOI to look up on Unpaywall, OpenAlex’s title search was out of its daily budget for this client, and the publisher sells it; no open copy is known. It stays Unavailable until a copy is supplied. |
| LIT-1683 | Unto Others: The Evolution and Psychology of Unselfish Behavior | Sober & Wilson (1998). Part I defends multilevel (group) selection as a cause of evolutionary altruism; Part II argues that the case for psychological egoism fails and that natural selection likely produced genuinely other-directed ultimate desires, distinguishing evolutionary from psychological altruism. | Unavailable — filed 2026-10-29; reading attempted the same day, no lawful copy reached. The Internet Archive’s copy (untoothersevolut00sobe) is for print-disabled readers only and is not lent, and no open edition was found. No NOTE is filed. It stays Unavailable until a copy is supplied (ADR-041). Read in its place, and not a substitute for reading it: Stich 2006 (LIT-1737). |
| LIT-1704 | Human transgenerational responses to early-life experience: potential impact on development, health and biomedical research | Pembrey, Saffery and Bygren (2014). A position paper by an 18-member network, two of whose authors led the Överkalix studies. It uses “transgenerational” for any outcome in offspring of an exposure in a parent before conception or in an earlier ancestor. In Överkalix cohorts of about 100 people each, a paternal grandfather’s good food supply in mid-childhood went with higher mortality in his grandsons (rate ratio 1.67) and poor supply with lower (0.65); for paternal grandmothers and granddaughters, 2.13 and 0.72. In ALSPAC, sons of fathers who began smoking before 11 carried more fat from age 13. The authors answer the charge of multiple testing with prior hypotheses and coherence across studies, grant that replication is needed, and hold that a sensitive period in the grandparent’s mid-childhood, not adolescence, makes cultural or genetic inheritance alone unlikely. They stay agnostic on mechanism and ask cohorts to collect ancestral exposure data. | Active — read in full 2026-10-29 (NOTE-1320), in place of LIT-1764, which could not be fetched here; worth reading as the Överkalix authors’ own later account of their findings and of how they answer the charges of multiple testing and cultural confounding. |
| LIT-1737 | Evolution, altruism and cognitive architecture: a critique of Sober and Wilson’s argument for psychological altruism | Stich (2006/2007). Restates Sober and Wilson’s argument that natural selection is unlikely to have made us pure egoists: for parental care, an ultimate desire for the child’s welfare is a more reliable mechanism than hedonism, which depends on beliefs linking helping to one’s own pleasure and pain. Stich rejects three of their four arguments outright. The fourth, that hedonism’s linking beliefs could be undermined by evidence, fails if the links are sticky sub-doxastic states. So the argument leaves egoism open; it does not show it true. | Active — read in full 2026-10-29 (NOTE-1282) from the published version on Stich’s own site; worth reading as a close restatement and critique of Sober and Wilson’s evolutionary argument for psychological altruism, read in place of Unto Others (LIT-1683, Unavailable), and for its definitions of egoism, altruism and ultimate desire, which the owner’s thesis (CLAIM-491) has to meet. |
| LIT-1821 v2 | The Organism as a System: Insights from Paul Weiss | Nicholson (2026) reconstructs from the writings of the experimental biologist Paul Weiss (1898–1989) a non-formal concept of a system: a whole that keeps its configuration while its parts vary and turn over, whose parts are produced and constrained by the network they form (a triplet of processes each supplying conditions for the other two, no pair viable without the third), and which cannot be assembled stepwise or recovered from an inventory of its parts. He turns it against reductionism, genocentrism, determinism and mechanicism. The critiques are argued by analogy and conceptual analysis; only the one against determinism cites evidence, and none is presented in the paper. Weiss’s one formula, that the whole varies far less than its parts’ summed variances, is met by any aggregate whose whole is an average. | Active — read in full 2026-10-29 (NOTE-1340) from the Europe PMC full text; worth reading as the clearest gathering of Weiss’s system concept and of its triplet of mutually producing processes, an early statement of closure, and for its four critiques, of which only the one against determinism rests on cited evidence. |
| LIT-1861 | Can populations be healthy? Perspectives from Georges Canguilhem and Geoffrey Rose | Giroux (2021), HPLS 43:111. Canguilhem held that health and disease apply only to individuals taken as organic totalities, because normativity, the capacity to institute new norms, is anchored in the organism; at the population level he preferred “hygiene” or “salubrity”. Giroux argues that debates over units of selection and biological individuality loosen his link between individuality and organism, and that social epidemiology (Rose’s causes of incidence, integral variables such as herd immunity and social capital, multilevel models) gives reasons for a concept of population health not reducible to individual health, while denying populations the ontological unity of an organism. | Active — read in full 2026-10-30 (NOTE-1452), from the published article in PubMed Central (PMC8527978; made available in the PMC Open Access Subset under Springer Nature’s COVID-19 terms), fetched as XML through the Europe PMC REST API. Worth reading for two things. It argues, from social epidemiology (Rose’s population causes, herd immunity, integral variables), that some health properties belong to populations and not to their members, against Canguilhem’s restriction of health to the individual organism. And it quotes Canguilhem’s definition of health as normativity in his own (translated) words: “the possibility of tolerating infractions of the habitual norm and instituting new norms in new situations” (The Normal and the Pathological, 1991, pp. 196–197). The Canguilhem it reports is at second hand. |
| LIT-1865 v2 | What makes biological organisation teleological? | Mossio and Bich (2014; Synthese 194, 2017, 1089–1114). Biological organisation is intrinsically teleological because it self-determines as self-constraint: closure, a set of mutually dependent constraints that canalise a far-from-equilibrium flow at another level of causation. A cycle of transformations such as the water cycle is not closure. Dissipative structures do not realise closure; at most, on a contested reading, they make one macroscopic constraint and are minimally teleological, unorganised and without functions. Read for THEORY-072. | Active — read in full on 2026-10-30 (NOTE-1443) from the authors’ accepted manuscript on HAL, hal.science/hal-01137522 (CC BY-NC 4.0), fetched from hal.science/hal-01137522/document. The PhilSci-Archive copy (philsci-archive.pitt.edu/11156) failed TLS verification from this client the same day and was not used. Worth reading as the authors’ own statement, a year before LIT-582, that closure of constraints already carries the division of labour, and that dissipative structures do not realise closure but at most make a single macroscopic constraint. |
| LIT-1876 | Reasoning in Life: Values and Normativity in Georges Canguilhem | Vissio (2020), Int J Semiot Law 33:1019–1031. Canguilhem’s vitalism is neither metaphysical nor structural–functional but “attitudinal”: life is a normative activity of evaluating a milieu. To be sick is not to lack norms but to be reduced in the capacity to change them; “normativity” is that capacity. Social norms differ in kind from vital ones (they are “to be invented and not observed”), so there is no social pathology, yet human reason and science are answers to a vital exigency. Proposed as a ground for a semiotics of values. | Active — read in full 2026-10-30 (NOTE-1447), from the open-access published article (CC BY 4.0) in PubMed Central, PMC7678399, fetched as XML through the Europe PMC REST API. A short exposition of Canguilhem’s philosophy of norms as an “attitudinal” vitalism. Worth reading for its account of normativity in his words: the sick organism is “confined and reduced in its capacity to change” its norms, and “normativity” is the name for “this ability or capacity to redefine vital norms”, with quotations from The Normal and the Pathological. It also reports his argument that social norms differ in kind from vital ones, so that there is no social pathology. Canguilhem at second hand; no argument of Vissio’s own beyond the reading. |
| LIT-1888 v2 | Theoretical principles for biology: Organization | Mossio, Montévil & Longo (2016). Proposes organization, understood as closure of constraints, as one of two theoretical principles for biology, beside variation, which a companion paper treats. The principles are posited a priori, as physics posits its phase space, and they define the domain: any system meeting both is biological, organisms being one class. The paper restates Montévil and Mossio’s definitions of constraint, dependence and closure. It argues, without a model, that closure grounds stability by regenerating constraints beyond their own time scales, and that it also propagates variation, so a change that reaches a constraint’s generators ends in disintegration or a new closure. | Active — read in full 2026-10-31 (NOTE-1461) from the authors’ HAL deposit; worth reading for the status it gives closure of constraints, a theoretical principle that defines the domain of biology rather than an empirical finding about organisms (THEORY-1251), and for its argument that closure both removes and propagates variation (THEORY-1271). It adds no formal content to Montévil and Mossio 2015 (LIT-582), and its stability claims are argued without a model. |
| LIT-1927 | Evolutionary Transitions in Individuality by Endogenization of Scaffolded Properties | Bourrat (2022 online; 2025 in print), DOI-10.1086/719118. As Griesemer and Shavit report it (LIT-188, §2), a transition in individuality can start from ecological scaffolding that imposes Darwinian properties on collectives from outside, and it completes only when the collectives “endogenize” those properties, so that they survive release from the scaffold; otherwise the collective is “de-Darwinized”. Unread here. | Deferred — filed 2026-11-01, not read. Registered because Griesemer and Shavit (LIT-188, §2) build their “missing ingredient” on it. OpenAlex marks it open access (hybrid) at the publisher. No reading was attempted. |
| LIT-1932 | Development, Culture, and the Units of Inheritance | Griesemer (2000), DOI-10.1086/392831. Against developmental systems theory’s expanded replicator, an account of inheritance as reproduction with material overlap and development, which yields a new unit, the reproducer, in which genetic and developmental roles cannot be separated. From the abstract; unread. | Deferred — filed 2026-11-01, not read. Registered because Griesemer and Shavit’s account of community reproduction (LIT-188, §3) is this paper’s account of inheritance carried to social groups. OpenAlex reports it closed; a CiteSeerX record of a submitted version is listed there and was not tried. |
| LIT-1935 | Can models of evolutionary transition clarify the debates over the Neolithic Revolution? | Shavit & Sharon (2023), DOI-10.1098/rstb.2021.0413. Asks whether an evolutionary-transition-in-individuality perspective can clarify the disputed cause, tempo and role of intention in the Neolithic shift in the southern Levant; it offers “a fresh lens”, not a solution, stressing within- and between-group differences. From the abstract; unread. | Deferred — filed 2026-11-01, not read. The companion paper to LIT-188 in the same theme issue, and the source of its one worked illustration. Open access (CC BY) at PubMed Central as PMC9869441; no reading was attempted. |
| LIT-1936 | Dynamic mechanistic explanation: computational modeling of circadian rhythms as an exemplar for cognitive science | Bechtel & Abrahamsen (2010). Dynamic mechanistic explanation adds to a mechanistic account a computational model, usually differential equations in time, whose variables are properties of the mechanism’s parts and operations. In circadian research the parts were found first by experiment, and the models explore their dynamics. In cognitive science the models posit the mechanism de novo, and fit to behaviour is their only check. The paper names six contributions models make, from showing that an identified mechanism can produce the phenomenon (C1) to exploring how coupled mechanisms lose and regain synchrony (C6). Its limit, in its own words: for de novo models, “Empirical evidence can rule out specific models, but usually cannot decide between competing architectures.” | Active — read in full 2026-11-01 (NOTE-1492); worth keeping for the line it draws between a dynamical model whose variables are anchored to parts and operations already found by experiment, and one posited de novo that is checked only by fit to behaviour (THEORY-1290). Kept also for two uses of modelling that bear on the record’s maintenance constructions. One is clamping a variable to test whether an identified part belongs to the responsible mechanism (THEORY-1289). The other is the open question whether peripheral circadian clocks sustain their own rhythm or are damped oscillators driven from outside (THEORY-1292). |
| LIT-1937 | The Units of Evolutionary Transition | Griesemer (2000/2001), DOI-10.1556/Select.1.2000.1-3.7. Maynard Smith’s principle of multiplication is elaborated into a general account of reproduction integrating heredity and development at every level of the hierarchy; this yields the reproducer, generalizing the replicator, and a revised theory of evolutionary transitions with a three-stage scenario. From the abstract; unread. | Deferred — filed 2026-11-01, not read. Registered because it is the source of the reproducer-based account of transitions that Griesemer and Shavit (LIT-188, §2) lean on to treat demic groups as candidate higher-level reproducers. OpenAlex reports it closed. No reading was attempted. |
| LIT-1940 | Ecological scaffolding and the evolution of individuality | Black, Bourrat & Rainey (2020), DOI-10.1038/s41559-019-1086-9. A model in which an ecological scaffold, patchy resources with a regime of dispersal, imposes Darwinian properties on collectives of cells before any collective-level mechanism exists, so that selection can act on collectives from the start. Unread here; described from LIT-188 §2 and the record’s Bourrat readings. | Deferred — filed 2026-11-01, not read. Registered as the model Bourrat’s endogenization account and Griesemer and Shavit’s §2 (LIT-188) rest on. No reading was attempted. |
| LIT-2001 v2 | The Major Transitions in Evolution | Maynard Smith & Szathmáry (1995; OUP edition 1997), doi:10.1093/oso/9780198502944.001.0001. Registered unread from the owner’s synthesis of 2026-11-04, which names it as the origin of major evolutionary transitions theory and that theory as the bridge between coexistence, endosymbiosis, game theory and morality. The record has held the theory only through Okasha’s reading of it (LIT-749, NOTE-586). | Unavailable — searched 2026-11-04 for a lawful full text, and none was found, so it is not read and no NOTE is filed. OpenAlex (no email address sent, ADR-008) reports the book closed, with no repository holding a full text. Its only location is Oxford Academic, which is paywalled. The companion Nature article (Szathmáry and Maynard Smith 1995, doi:10.1038/374227a0) is closed as well. A copy the owner supplies returns it to reading. |
| LIT-2003 v2 | Major evolutionary transitions in individuality | West, Fisher, Gardner & Kiers (2015), doi:10.1073/pnas.1421402112. A transition in individuality is defined by mutual dependence and negligible within-group conflict, which Table 1 shows occur apart. It proceeds by forming a cooperative group and then transforming it, with no clear border between the steps. An ecological benefit together with how groups form explains the transitions; kin discrimination and repression of competition played minor roles. Source of THEORY-1351, read in NOTE-1538. | Active |